Starting phenix.real_space_refine on Sun Mar 10 16:50:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd4_38265/03_2024/8xd4_38265_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd4_38265/03_2024/8xd4_38265.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd4_38265/03_2024/8xd4_38265_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd4_38265/03_2024/8xd4_38265_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd4_38265/03_2024/8xd4_38265_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd4_38265/03_2024/8xd4_38265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd4_38265/03_2024/8xd4_38265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd4_38265/03_2024/8xd4_38265_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd4_38265/03_2024/8xd4_38265_neut_updated.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2115 2.51 5 N 568 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3342 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3288 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 418, 3277 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 418, 3277 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3338 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 54 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 11} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 118 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 118 " occ=0.50 Time building chain proxies: 4.06, per 1000 atoms: 1.21 Number of scatterers: 3342 At special positions: 0 Unit cell: (69.184, 75.952, 71.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 642 8.00 N 568 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 1.3 seconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 3 sheets defined 49.0% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.770A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.534A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.602A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.487A pdb=" N ASP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASN A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 360 removed outlier: 3.538A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.624A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.240A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.829A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 162 hydrogen bonds defined for protein. 471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1087 1.34 - 1.46: 674 1.46 - 1.57: 1616 1.57 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3406 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.568 0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" C4A NAP A 500 " pdb=" N3A NAP A 500 " ideal model delta sigma weight residual 1.332 1.439 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C8A NAP A 500 " pdb=" N7A NAP A 500 " ideal model delta sigma weight residual 1.301 1.399 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C6A NAP A 500 " pdb=" N6A NAP A 500 " ideal model delta sigma weight residual 1.335 1.433 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C8A NAP A 500 " pdb=" N9A NAP A 500 " ideal model delta sigma weight residual 1.371 1.463 -0.092 2.00e-02 2.50e+03 2.12e+01 ... (remaining 3401 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.52: 107 106.52 - 113.41: 1861 113.41 - 120.30: 1205 120.30 - 127.19: 1405 127.19 - 134.08: 47 Bond angle restraints: 4625 Sorted by residual: angle pdb=" O THR A 302 " pdb=" C THR A 302 " pdb=" N GLU A 303 " ideal model delta sigma weight residual 122.94 116.83 6.11 1.37e+00 5.33e-01 1.99e+01 angle pdb=" O1A NAP A 500 " pdb=" PA NAP A 500 " pdb=" O2A NAP A 500 " ideal model delta sigma weight residual 121.77 109.61 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O1N NAP A 500 " pdb=" PN NAP A 500 " pdb=" O2N NAP A 500 " ideal model delta sigma weight residual 122.51 110.60 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CA THR A 302 " pdb=" C THR A 302 " pdb=" N GLU A 303 " ideal model delta sigma weight residual 115.42 121.67 -6.25 1.64e+00 3.72e-01 1.45e+01 angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 119.32 123.59 -4.27 1.14e+00 7.69e-01 1.40e+01 ... (remaining 4620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 1791 16.79 - 33.58: 181 33.58 - 50.37: 53 50.37 - 67.15: 22 67.15 - 83.94: 14 Dihedral angle restraints: 2061 sinusoidal: 860 harmonic: 1201 Sorted by residual: dihedral pdb=" CA ASP A 340 " pdb=" CB ASP A 340 " pdb=" CG ASP A 340 " pdb=" OD1 ASP A 340 " ideal model delta sinusoidal sigma weight residual -30.00 -87.65 57.65 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA BARG A 118 " pdb=" CB BARG A 118 " pdb=" CG BARG A 118 " pdb=" CD BARG A 118 " ideal model delta sinusoidal sigma weight residual -180.00 -121.07 -58.93 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLN A 19 " pdb=" CA GLN A 19 " pdb=" CB GLN A 19 " pdb=" CG GLN A 19 " ideal model delta sinusoidal sigma weight residual 60.00 117.02 -57.02 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 2058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 413 0.059 - 0.118: 80 0.118 - 0.177: 7 0.177 - 0.236: 1 0.236 - 0.295: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" C2B NAP A 500 " pdb=" C1B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" O2B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASP A 133 " pdb=" N ASP A 133 " pdb=" C ASP A 133 " pdb=" CB ASP A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA LYS A 391 " pdb=" N LYS A 391 " pdb=" C LYS A 391 " pdb=" CB LYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 499 not shown) Planarity restraints: 590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 302 " -0.014 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C THR A 302 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 302 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 303 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AARG A 118 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C AARG A 118 " 0.039 2.00e-02 2.50e+03 pdb=" O AARG A 118 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 119 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BARG A 118 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" C BARG A 118 " 0.039 2.00e-02 2.50e+03 pdb=" O BARG A 118 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 119 " -0.013 2.00e-02 2.50e+03 ... (remaining 587 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1096 2.84 - 3.35: 3202 3.35 - 3.87: 5843 3.87 - 4.38: 6792 4.38 - 4.90: 11459 Nonbonded interactions: 28392 Sorted by model distance: nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.325 2.440 nonbonded pdb=" OG1 THR A 175 " pdb=" OG SER A 351 " model vdw 2.356 2.440 nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.406 2.440 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.412 2.520 nonbonded pdb=" O THR A 189 " pdb=" OG1 THR A 189 " model vdw 2.415 2.440 ... (remaining 28387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.530 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 3406 Z= 0.503 Angle : 0.824 12.161 4625 Z= 0.452 Chirality : 0.047 0.295 502 Planarity : 0.005 0.056 590 Dihedral : 17.180 83.942 1295 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.81 % Allowed : 2.35 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.42), residues: 419 helix: 2.22 (0.34), residues: 211 sheet: -0.35 (0.70), residues: 60 loop : -0.62 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.001 0.000 HIS A 394 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 225 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.384 Fit side-chains REVERT: A 46 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8724 (mmm) REVERT: A 149 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8286 (p0) REVERT: A 351 SER cc_start: 0.9125 (t) cc_final: 0.8879 (m) outliers start: 12 outliers final: 2 residues processed: 97 average time/residue: 1.2837 time to fit residues: 127.6706 Evaluate side-chains 61 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3406 Z= 0.191 Angle : 0.531 7.211 4625 Z= 0.272 Chirality : 0.044 0.177 502 Planarity : 0.005 0.046 590 Dihedral : 9.924 58.817 513 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.64 % Allowed : 16.13 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.43), residues: 419 helix: 2.59 (0.36), residues: 210 sheet: 0.16 (0.70), residues: 60 loop : -0.48 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 PHE 0.011 0.002 PHE A 341 TYR 0.013 0.001 TYR A 225 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.9124 (mmt) cc_final: 0.8905 (mmt) REVERT: A 267 HIS cc_start: 0.7137 (m170) cc_final: 0.5558 (m170) REVERT: A 351 SER cc_start: 0.9135 (t) cc_final: 0.8899 (m) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.9718 time to fit residues: 69.5273 Evaluate side-chains 63 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 307 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3406 Z= 0.264 Angle : 0.546 7.115 4625 Z= 0.278 Chirality : 0.046 0.155 502 Planarity : 0.005 0.045 590 Dihedral : 9.052 59.277 504 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.40 % Favored : 97.36 % Rotamer: Outliers : 3.81 % Allowed : 16.42 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.43), residues: 419 helix: 2.40 (0.36), residues: 213 sheet: 0.15 (0.74), residues: 55 loop : -0.57 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.008 0.002 HIS A 267 PHE 0.013 0.002 PHE A 341 TYR 0.015 0.002 TYR A 250 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 351 SER cc_start: 0.9119 (t) cc_final: 0.8915 (m) outliers start: 12 outliers final: 5 residues processed: 69 average time/residue: 1.0744 time to fit residues: 76.6116 Evaluate side-chains 64 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3406 Z= 0.188 Angle : 0.511 6.552 4625 Z= 0.259 Chirality : 0.045 0.144 502 Planarity : 0.004 0.044 590 Dihedral : 8.690 59.185 504 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Rotamer: Outliers : 2.93 % Allowed : 18.18 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.43), residues: 419 helix: 2.45 (0.35), residues: 212 sheet: 0.21 (0.75), residues: 55 loop : -0.53 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.007 0.002 HIS A 267 PHE 0.011 0.001 PHE A 341 TYR 0.012 0.001 TYR A 225 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8620 (mtmt) REVERT: A 263 TRP cc_start: 0.8344 (t-100) cc_final: 0.8131 (t-100) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 1.1063 time to fit residues: 76.7317 Evaluate side-chains 61 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 328 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3406 Z= 0.202 Angle : 0.504 6.032 4625 Z= 0.255 Chirality : 0.045 0.141 502 Planarity : 0.004 0.044 590 Dihedral : 8.534 59.131 504 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.40 % Favored : 97.36 % Rotamer: Outliers : 3.23 % Allowed : 18.18 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.43), residues: 419 helix: 2.42 (0.35), residues: 213 sheet: 0.01 (0.75), residues: 57 loop : -0.54 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.002 HIS A 267 PHE 0.011 0.001 PHE A 341 TYR 0.011 0.001 TYR A 408 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8630 (mtmt) REVERT: A 263 TRP cc_start: 0.8364 (t-100) cc_final: 0.8137 (t-100) outliers start: 10 outliers final: 4 residues processed: 64 average time/residue: 1.0228 time to fit residues: 67.8125 Evaluate side-chains 60 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 328 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3406 Z= 0.174 Angle : 0.496 7.263 4625 Z= 0.250 Chirality : 0.044 0.177 502 Planarity : 0.004 0.044 590 Dihedral : 8.320 58.741 504 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.64 % Favored : 97.12 % Rotamer: Outliers : 2.35 % Allowed : 20.23 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.43), residues: 419 helix: 2.56 (0.35), residues: 211 sheet: -0.00 (0.75), residues: 57 loop : -0.66 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 267 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 225 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8371 (t-100) cc_final: 0.8139 (t-100) REVERT: A 419 LYS cc_start: 0.7611 (ttmt) cc_final: 0.7396 (mtpm) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 1.0561 time to fit residues: 68.8202 Evaluate side-chains 62 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.0000 overall best weight: 1.1846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3406 Z= 0.162 Angle : 0.491 6.321 4625 Z= 0.245 Chirality : 0.044 0.154 502 Planarity : 0.004 0.044 590 Dihedral : 8.178 58.913 504 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.64 % Favored : 97.12 % Rotamer: Outliers : 2.35 % Allowed : 20.23 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.43), residues: 419 helix: 2.72 (0.36), residues: 205 sheet: -0.02 (0.62), residues: 79 loop : -0.14 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 267 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 408 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 263 TRP cc_start: 0.8382 (t-100) cc_final: 0.8154 (t-100) REVERT: A 419 LYS cc_start: 0.7614 (ttmt) cc_final: 0.7404 (mtpm) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.9970 time to fit residues: 67.2606 Evaluate side-chains 64 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3406 Z= 0.141 Angle : 0.477 5.888 4625 Z= 0.240 Chirality : 0.043 0.144 502 Planarity : 0.004 0.044 590 Dihedral : 8.037 59.477 504 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Rotamer: Outliers : 1.17 % Allowed : 21.70 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.43), residues: 419 helix: 2.75 (0.36), residues: 205 sheet: 0.00 (0.60), residues: 81 loop : -0.11 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 267 PHE 0.009 0.001 PHE A 341 TYR 0.010 0.001 TYR A 225 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.390 Fit side-chains REVERT: A 263 TRP cc_start: 0.8356 (t-100) cc_final: 0.8124 (t-100) REVERT: A 419 LYS cc_start: 0.7543 (ttmt) cc_final: 0.7337 (mtpm) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 0.9442 time to fit residues: 59.8719 Evaluate side-chains 62 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 328 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 8.9990 chunk 33 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 0.0070 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3406 Z= 0.128 Angle : 0.476 5.972 4625 Z= 0.239 Chirality : 0.043 0.139 502 Planarity : 0.004 0.043 590 Dihedral : 7.890 59.901 504 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.64 % Favored : 97.12 % Rotamer: Outliers : 1.17 % Allowed : 21.70 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.43), residues: 419 helix: 2.76 (0.36), residues: 206 sheet: -0.03 (0.59), residues: 81 loop : -0.07 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.005 0.001 HIS A 267 PHE 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 250 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.385 Fit side-chains REVERT: A 263 TRP cc_start: 0.8344 (t-100) cc_final: 0.8105 (t-100) REVERT: A 419 LYS cc_start: 0.7479 (ttmt) cc_final: 0.7245 (mtpm) outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 1.0286 time to fit residues: 65.0143 Evaluate side-chains 61 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3406 Z= 0.126 Angle : 0.462 5.672 4625 Z= 0.232 Chirality : 0.043 0.130 502 Planarity : 0.004 0.043 590 Dihedral : 7.698 59.089 504 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.64 % Favored : 97.12 % Rotamer: Outliers : 0.88 % Allowed : 21.99 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.43), residues: 419 helix: 2.81 (0.35), residues: 206 sheet: -0.03 (0.61), residues: 79 loop : -0.14 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 267 PHE 0.009 0.001 PHE A 341 TYR 0.011 0.001 TYR A 408 ARG 0.004 0.000 ARG A 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.323 Fit side-chains REVERT: A 284 LEU cc_start: 0.8570 (tt) cc_final: 0.8313 (tp) REVERT: A 419 LYS cc_start: 0.7532 (ttmt) cc_final: 0.7295 (mtpm) outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 1.0266 time to fit residues: 65.8704 Evaluate side-chains 60 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 0.0070 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.135534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.096748 restraints weight = 12731.294| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.97 r_work: 0.2720 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3406 Z= 0.132 Angle : 0.460 5.348 4625 Z= 0.233 Chirality : 0.043 0.128 502 Planarity : 0.004 0.043 590 Dihedral : 7.530 58.546 502 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.64 % Favored : 97.12 % Rotamer: Outliers : 0.59 % Allowed : 22.87 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.43), residues: 419 helix: 2.82 (0.35), residues: 206 sheet: 0.05 (0.64), residues: 74 loop : -0.16 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.004 0.001 HIS A 267 PHE 0.009 0.001 PHE A 341 TYR 0.009 0.001 TYR A 250 ARG 0.007 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1864.73 seconds wall clock time: 33 minutes 42.39 seconds (2022.39 seconds total)